{"id":"https://openalex.org/W1986656046","doi":"https://doi.org/10.1371/journal.pcbi.1000308","title":"GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions","display_name":"GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions","publication_year":2009,"publication_date":"2009-03-12","ids":{"openalex":"https://openalex.org/W1986656046","doi":"https://doi.org/10.1371/journal.pcbi.1000308","mag":"1986656046"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000308","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000308","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000308&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000308&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100460647","display_name":"Vinay Kumar","orcid":"https://orcid.org/0000-0003-0077-0956"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vinay Satish Kumar","raw_affiliation_strings":["Department of Industrial and Manufacturing Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Industrial and Manufacturing Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083581014","display_name":"Costas D. Maranas","orcid":"https://orcid.org/0000-0002-1508-1398"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Costas D. Maranas","raw_affiliation_strings":["Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5083581014"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":8.7622,"has_fulltext":true,"cited_by_count":216,"citation_normalized_percentile":{"value":0.98492391,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"5","issue":"3","first_page":"e1000308","last_page":"e1000308"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10171","display_name":"Biofuel production and bioconversion","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.9102228879928589},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.7561709880828857},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.5992045998573303},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5347081422805786},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5042182207107544},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.4509281516075134},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.44278356432914734},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3836929500102997},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.36671555042266846},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33887404203414917},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2303161919116974},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1919555366039276}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.9102228879928589},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.7561709880828857},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.5992045998573303},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5347081422805786},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5042182207107544},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.4509281516075134},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.44278356432914734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3836929500102997},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.36671555042266846},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33887404203414917},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2303161919116974},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1919555366039276}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1000308","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000308","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000308&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.554.3593","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.554.3593","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://maranas.che.psu.edu/pub/satishkumar-maranas09.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:36ee252ee1244f03a4c7967326e6c268","is_oa":true,"landing_page_url":"https://doaj.org/article/36ee252ee1244f03a4c7967326e6c268","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 5, Iss 3, p e1000308 (2009)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/148218","is_oa":true,"landing_page_url":"https://figshare.com/articles/GrowMatch_An_Automated_Method_for_Reconciling_In_Silico_In_Vivo_Growth_Predictions/148218","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2645679","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2645679","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000308","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000308","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000308&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G194141444","display_name":null,"funder_award_id":"DE-FG02-05ER25684","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2597931350","display_name":"DEVELOPMENT OF COMPUTATIONAL TOOLS FOR ANALYZING AND REDESIGNING METABOLIC NETWORKS","funder_award_id":"FG02-05ER25684","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5219260752","display_name":null,"funder_award_id":"DE-FG","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7186324567","display_name":null,"funder_award_id":"DE-FG02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8684078510","display_name":null,"funder_award_id":"DE-FG02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1986656046.pdf","grobid_xml":"https://content.openalex.org/works/W1986656046.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1597762351","https://openalex.org/W1603241183","https://openalex.org/W1814099126","https://openalex.org/W1974482866","https://openalex.org/W1982309495","https://openalex.org/W1985687822","https://openalex.org/W1991972770","https://openalex.org/W2006672203","https://openalex.org/W2009940763","https://openalex.org/W2014348203","https://openalex.org/W2022012525","https://openalex.org/W2025663053","https://openalex.org/W2026904316","https://openalex.org/W2045780029","https://openalex.org/W2048214825","https://openalex.org/W2052464097","https://openalex.org/W2068204754","https://openalex.org/W2073837631","https://openalex.org/W2077896867","https://openalex.org/W2079048673","https://openalex.org/W2085236271","https://openalex.org/W2091393253","https://openalex.org/W2093975175","https://openalex.org/W2096245011","https://openalex.org/W2097002638","https://openalex.org/W2102164505","https://openalex.org/W2104108767","https://openalex.org/W2104619491","https://openalex.org/W2107459209","https://openalex.org/W2108078368","https://openalex.org/W2111031006","https://openalex.org/W2111967267","https://openalex.org/W2119215577","https://openalex.org/W2123060905","https://openalex.org/W2128601422","https://openalex.org/W2130085523","https://openalex.org/W2132757418","https://openalex.org/W2142237411","https://openalex.org/W2142437744","https://openalex.org/W2145996960","https://openalex.org/W2146538795","https://openalex.org/W2152488335","https://openalex.org/W2153373497","https://openalex.org/W2158784643","https://openalex.org/W2164997719","https://openalex.org/W2165674132","https://openalex.org/W2170427655","https://openalex.org/W2336167279","https://openalex.org/W2336259629","https://openalex.org/W3106353906","https://openalex.org/W4230392683","https://openalex.org/W6823566691"],"related_works":["https://openalex.org/W2912862995","https://openalex.org/W1995733425","https://openalex.org/W2148190806","https://openalex.org/W2170249521","https://openalex.org/W1576707484","https://openalex.org/W2573984017","https://openalex.org/W2165387703","https://openalex.org/W2900490993","https://openalex.org/W4385520263","https://openalex.org/W4378515658"],"abstract_inverted_index":{"Genome-scale":[0],"metabolic":[1,158,169,263],"reconstructions":[2],"are":[3],"typically":[4],"validated":[5],"by":[6,152,164,183,199,212],"comparing":[7],"in":[8,20,27,43,76,100,108,112,121,124,155,167],"silico":[9,101,122],"growth":[10,22,37,40,53,58],"predictions":[11,72,81,96,126],"across":[12],"different":[13,16],"mutants":[14,142,176,198],"utilizing":[15],"carbon":[17],"sources":[18],"with":[19,123],"vivo":[21,109,125],"data.":[23],"This":[24],"comparison":[25],"results":[26],"two":[28],"types":[29],"of":[30,97,120,189,222,256],"modelprediction":[31],"inconsistencies;":[32],"either":[33],"the":[34,44,49,55,77,86,95,98,107,113,118,156,168,172,186,203,206,220,223,253],"model":[35,50,105,204,233],"predicts":[36,51],"when":[38,54],"no":[39,52],"is":[41],"observed":[42],"experiment":[45,56],"(GNG":[46],"inconsistencies)":[47],"or":[48],"reveals":[57],"(NGG":[59],"inconsistencies).":[60],"Here":[61],"we":[62,132],"propose":[63],"an":[64],"optimization-based":[65],"framework,":[66],"GrowMatch,":[67],"to":[68,85,91,129,135,178,202,241,260,266],"automatically":[69],"reconcile":[70],"GNG":[71,141,150,175],"(by":[73,82],"suppressing":[74,165],"functionalities":[75,84,201],"model)":[78],"and":[79,106,116,143,171,269],"NGG":[80,145,197],"adding":[83,200],"model).":[87],"We":[88],"use":[89],"GrowMatch":[90,147,191,229,248],"resolve":[92],"inconsistencies":[93,151,161,209],"between":[94],"latest":[99],"Escherichia":[102],"coli":[103],"(iAF1260)":[104],"data":[110],"available":[111],"Keio":[114],"collection":[115],"improved":[117],"consistency":[119],"from":[127],"90.6%":[128],"96.7%.":[130],"Specifically,":[131],"were":[133,162,181,210],"able":[134],"suggest":[136],"consistency-restoring":[137],"hypotheses":[138,194,235],"for":[139,195],"56/72":[140],"13/38":[144],"mutants.":[146],"resolved":[148,163,182,211],"18":[149],"suggesting":[153],"suppressions":[154],"mutant":[157],"networks.":[159],"Fifteen":[160],"isozymes":[166],"network,":[170],"remaining":[173,207],"23":[174],"corresponding":[177],"blocked":[179],"genes":[180,216],"suitably":[184],"modifying":[185],"biomass":[187],"equation":[188],"iAF1260.":[190],"suggested":[192],"consistencyrestoring":[193],"five":[196],"whereas":[205],"eight":[208],"pinpointing":[213],"possible":[214],"alternate":[215],"that":[217,236],"carry":[218],"out":[219],"function":[221],"deleted":[224],"gene.":[225],"For":[226],"many":[227],"cases,":[228],"identified":[230],"fairly":[231],"nonintuitive":[232],"modification":[234],"would":[237],"have":[238],"been":[239],"difficult":[240],"pinpoint":[242],"through":[243],"inspection":[244],"alone.":[245],"In":[246],"addition,":[247],"can":[249],"be":[250],"used":[251],"during":[252],"construction":[254],"phase":[255],"new,":[257],"as":[258],"opposed":[259],"existing,":[261],"genome-scale":[262],"models,":[264],"leading":[265],"more":[267],"expedient":[268],"accurate":[270],"reconstructions.":[271]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":17},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":23},{"year":2016,"cited_by_count":20},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":17},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":23}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
